A Logistic Regression Approach for Identifying Hot Spots in Protein Interfaces

Author(s):  
Peipei Li ◽  
Keun Ho Ryu
2019 ◽  
Vol 139 (3) ◽  
pp. 235-245
Author(s):  
Carlos Augusto Ferreira Lobão ◽  
Letícia Miquilini ◽  
Breno Simões Ribeiro da Silva ◽  
Verônica Gabriela Ribeiro da Silva ◽  
Eliza Maria da Costa Brito Lacerda ◽  
...  

2019 ◽  
Vol 108 ◽  
pp. 182-195 ◽  
Author(s):  
Elisa Cuadrado-Godia ◽  
Ankush D. Jamthikar ◽  
Deep Gupta ◽  
Narendra N. Khanna ◽  
Tadashi Araki ◽  
...  

2018 ◽  
Vol 8 (1) ◽  
pp. 16 ◽  
Author(s):  
Irina Matijosaitiene ◽  
Peng Zhao ◽  
Sylvain Jaume ◽  
Joseph Gilkey Jr

Predicting the exact urban places where crime is most likely to occur is one of the greatest interests for Police Departments. Therefore, the goal of the research presented in this paper is to identify specific urban areas where a crime could happen in Manhattan, NY for every hour of a day. The outputs from this research are the following: (i) predicted land uses that generates the top three most committed crimes in Manhattan, by using machine learning (random forest and logistic regression), (ii) identifying the exact hours when most of the assaults are committed, together with hot spots during these hours, by applying time series and hot spot analysis, (iii) built hourly prediction models for assaults based on the land use, by deploying logistic regression. Assault, as a physical attack on someone, according to criminal law, is identified as the third most committed crime in Manhattan. Land use (residential, commercial, recreational, mixed use etc.) is assigned to every area or lot in Manhattan, determining the actual use or activities within each particular lot. While plotting assaults on the map for every hour, this investigation has identified that the hot spots where assaults occur were ‘moving’ and not confined to specific lots within Manhattan. This raises a number of questions: Why are hot spots of assaults not static in an urban environment? What makes them ‘move’—is it a particular urban pattern? Is the ‘movement’ of hot spots related to human activities during the day and night? Answering these questions helps to build the initial frame for assault prediction within every hour of a day. Knowing a specific land use vulnerability to assault during each exact hour can assist the police departments to allocate forces during those hours in risky areas. For the analysis, the study is using two datasets: a crime dataset with geographical locations of crime, date and time, and a geographic dataset about land uses with land use codes for every lot, each obtained from open databases. The study joins two datasets based on the spatial location and classifies data into 24 classes, based on the time range when the assault occurred. Machine learning methods reveal the effect of land uses on larceny, harassment and assault, the three most committed crimes in Manhattan. Finally, logistic regression provides hourly prediction models and unveils the type of land use where assaults could occur during each hour for both day and night.


2019 ◽  
Author(s):  
Amaurys Ibarra ◽  
Gail J. Bartlett ◽  
Zsofia Hegedus ◽  
Som Dutt ◽  
Fruzsina Hobor ◽  
...  

Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be applied to single structures from crystallography, and to structural ensembles from NMR or molecular dynamics data. The comparative analyses facilitate accurate prediction of hot-spots that we validate experimentally with three diverse targets: NOXA-B/MCL-1 (an α helix-mediated PPI), SIMS/SUMO and GKAP/SHANK-PDZ (both β strand-mediated interactions). Finally, the approach is applied to the accurate prediction of hot-residues at a topographically novel Affimer/BCL-xL protein-protein interface.


2020 ◽  
Vol 18 (3) ◽  
pp. 363-382
Author(s):  
Aleksandra K. Bordunos ◽  
◽  
Sofia V. Kosheleva ◽  
Anna Zyryanova ◽  
◽  
...  

This paper aims to identify the determinants of return to work after maternity leave in Russia. Can an organisation influence employees’ decision about withdrawal from the market after leave arrangement, or does it fully depend on the contextual and personal characteristics of the employee, as assumed by the discourses of merit and choice? Logistic regression analysis helps to answer the raised questions, referring to responses of 721 mothers with previous working experience. The research revealed that employers indeed can improve inclusion of employees with childcare commitments, fostering their return after the maternity leave. Despite high regional diversity of Russian population, contextual specificity barely influences the decision of employees regarding their returning to work with the same employer, similarly to their level of education, firms’ equity or amount of children. Among personal characteristics, income was found to play an important role in return decisions, as well as the age of the smallest child. The paper contributes to the debates on the fluidity of gender and work identity as well as organizational control over the identity work.


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